I am trying to create a variety of heatmaps of DESeq2 DEGlists to answer different questions. I have been using pheatmap.
This is my code so far:
dds <- DESeqDataSetFromMatrix(countData = cts,colData = coldata,design = ~Genotype) dds <- DESeq(dds) GRBrainResults <- results(dds,alpha = 0.05)
This is to sort the dataset by lowest padj value first
ndx = order(GRBrainResults$padj, decreasing = FALSE) GRBrainResultspadj <- GRBrainResultsSig[ndx,] head(GRBrainResultspadj,5) padj <numeric> ENSDARG00000028396 9.31612e-230 ENSDARG00000025428 2.31820e-176 ENSDARG00000059815 1.67438e-98 ENSDARG00000007693 3.58104e-80 ENSDARG00000087303 6.11981e-62 rld = rlogTransformation(dds)
I would like to create a heatmap of the top 30 most significant genes. I have been using pheatmap. I can create a heatmap, but the list of genes is not in the same order. Is this because they are clustering? If so, can somebody help me remove the row clustering please. This is what I have been using:
mat = assay(rld)[ head(order(GRBrainResults$padj),30), ] mat = mat - rowMeans(mat) df = as.data.frame(colData(rld)[,c("Genotype")]) colnames(df) = "Genotype" rownames(df) = colnames(mat) pheatmap(mat, annotation_col=df)
I produce a heatmap but its not in order, I see they logically clustered so figured this is it.
Can somebody please help me remove the row clustering?